Odds are you don't need to fret much about that side as you aren't seeing a lot of hp out of these motors. I think I would have just used sand paper and my thumb to knock down the edges of the pits so there are no sharp edges, then have a 3 way Serdi cut valve job and reassemble. Odds are she'll run fine. Then if it bothers you, keep an eye out for a CA95 head in better shape. These motors are easy to work on and it isn't a huge expense to do over if it needs it. I'm betting you'll be fine.
Now if you are going to race it, different story.
Go oversize on the pistons for a little more displacement would compensate for any compression loss.